Literature DB >> 19405565

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method.

Xiancheng Zeng1, Hao Hu, Xiangqian Hu, Weitao Yang.   

Abstract

A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids "on-the-fly" QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

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Year:  2009        PMID: 19405565      PMCID: PMC2736613          DOI: 10.1063/1.3120605

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  37 in total

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4.  Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase.

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Journal:  J Chem Phys       Date:  2006-03-28       Impact factor: 3.488

5.  Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures.

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Journal:  J Am Chem Soc       Date:  2006-02-01       Impact factor: 15.419

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7.  Diabatic free energy curves and coordination fluctuations for the aqueous Ag+Ag2+ redox couple: a biased Born-Oppenheimer molecular dynamics investigation.

Authors:  Jochen Blumberger; Ivano Tavernelli; Michael L Klein; Michiel Sprik
Journal:  J Chem Phys       Date:  2006-02-14       Impact factor: 3.488

8.  Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.

Authors:  Hao Hu; Zhenyu Lu; Jerry M Parks; Steven K Burger; Weitao Yang
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9.  Insights into current limitations of density functional theory.

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Journal:  Science       Date:  2008-08-08       Impact factor: 47.728

10.  Electronic structure and solvation of copper and silver ions: a theoretical picture of a model aqueous redox reaction.

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  10 in total

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Authors:  Ganglong Cui; Weitao Yang
Journal:  J Chem Phys       Date:  2011-05-28       Impact factor: 3.488

3.  Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways.

Authors:  Pan Wu; G Andrés Cisneros; Hao Hu; Robin Chaudret; Xiangqian Hu; Weitao Yang
Journal:  J Phys Chem B       Date:  2012-03-28       Impact factor: 2.991

4.  Fragment-based Quantum Mechanical/Molecular Mechanical Simulations of Thermodynamic and Kinetic Process of the Ru2+-Ru3+ Self-Exchange Electron Transfer.

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Journal:  J Chem Theory Comput       Date:  2012-12-11       Impact factor: 6.006

5.  Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

Authors:  Lin Shen; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2016-03-15       Impact factor: 6.006

6.  Noncovalent Interaction Analysis in Fluctuating Environments.

Authors:  Pan Wu; Robin Chaudret; Xiangqian Hu; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2013-05-14       Impact factor: 6.006

7.  Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants.

Authors:  Lin Shen; Xiancheng Zeng; Hao Hu; Xiangqian Hu; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2018-08-10       Impact factor: 6.006

Review 8.  Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

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Journal:  Nanomaterials (Basel)       Date:  2021-01-24       Impact factor: 5.076

9.  Redox Potentials of Disulfide Bonds in LOXL2 Studied by Nonequilibrium Alchemical Simulation.

Authors:  Lirui Lin; Haiying Zou; Wenjin Li; Li-Yan Xu; En-Min Li; Geng Dong
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10.  Complete mineralization of perfluorooctanoic acid (PFOA) by γ-irradiation in aqueous solution.

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Journal:  Sci Rep       Date:  2014-12-10       Impact factor: 4.379

  10 in total

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